Heikki Lehvaslaiho wrote:
>> Tim Cutts wrote:
> >
> > Has anyone written a parser for the LocusLink files?
> > (http://www.ncbi.nlm.nih.gov/LocusLink/refseq.html)
> >
> > The tabe delimited file LL.out looks easy, but the other file, which
> > contains the most information, looks a lot harder. Has anyone already
> > done this?
> >
> > Tim.
>> No. Not yet. but I'll have a go soon.
It's done. have a look at:
http://srs.ebi.ac.uk/srs5bin/cgi-bin/wgetz?-fun+PageQueryForm+-l+LOCUSLINK
I had to modify the field structure quite a bit to have a nice
listing, but that is done at runtime so does not matter.
The following is relevant only if you want ot copy the parsers into
your own server: In addition to creating the normal .i, .is and .it
files, I put two of $hrefs into srsgen.i:
# general entrez link
#db= m for medline, n for nucleotide, p for protein
# t for structure, c gor genome
#good defaults: form=6 & Dopt=g
$href:[entrezR link: |<A HREF="http://www.ncbi.nlm.nih.gov/\
|htbin-post/Entrez/query?\
|db=%s&uid=%s&form=%s&Dopt=%s">%s</A>\
]
$href:[unigeneR link:|<A
HREF=http://www.ncbi.nlm.nih.gov/cgi-bin/UniGene/\
|clust?ORG=%s&CID=%s>%s</A>
]
Also, to get a default view that somewhat duplicates NCBI's listing,
I added the following definition into views.i:
LocusLink_View:$View:[LocusLink
root:$Vlib:@LOCUSLINK_DB
rootFields:{
$VField:@DF_GeneName
$VField:@DF_Description
$VField:@DF_ChrLocation
$VField:@DF_LINK
}
]
Let me know if there is something I missed,
-Heikki
--
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_/ _/ _/ Heikki Lehvaslaiho heikki at ebi.ac.uk
_/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute
_/ _/ _/ Wellcome Trust Genome Campus, Hinxton
_/ _/ _/ Cambs. CB10 1SD, United Kingdom
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